Deceptions, Consequences and Choices
by forevershipper37
Summary: Jack and Sam eventually. Replicator Sam lets some stuff slip about Lt. Col. Carter and Jack decides to do something about it.
1. Chapter 1

So this idea came to me while I was drinking and binge watching Season 7 and part of season 8 yesterday. It starts with replicator Carter being introduced and goes on from there, with some hint of episodes following. That being said I have added a major plot twist/addition that will make it possible for Jack and Sam to get and stay together. Major Jack/Sam shipper and eventual Pete bashing.

As always, I do not own SG1 or it's characters.

Chapter 1

Jack was sitting in his chair contemplating what to do about the information he had been given when there was a knock on his door. "Enter. Carter, what can I do for you?" He watched as she closed the door behind her, locked it then proceeded to waltz over to him and plant a kiss on his lips. "What the-" he pushed her away. "I'm tired of pretending. This whole thing with 5th and the replicator me," she started as she straddled him. "I want you."

Jack pushed her off of him. "I don't think so."

She looked at him then shrugged. "It was worth a try. She is in love with you, you know."

Jack ignored her and stood. "What do you want?"

"She is," the replicator Carter continues. "She did her best to hide it while 5th was torturing her. But it's there. She's in love with you. She wonders if you still feel the same. There used to be times she could tell but lately, at least the lately that I was created, she couldn't. But her love for you is the main reason I got her to trust me. I showed her how 5th made me kill you over and over again as part of my training. After she got stuck on the Prometheus, she was going to quit then she was offered this black ops assignment. General Hammond doesn't even know. At least he didn't. She was ordered not to say anything though she wanted to tell you and the boys. Pete, they aren't really together, in fact Pete isn't even his real name. I don't know what it is. She held that one closer to her chest than her love for you. And this assignment that she's on—it has something to do with an assignment she was involved with before she found out about the Stargate. But she keeps that closely hidden too. There's a lot of hurt there. Still, I think she plans to quit when she's finished the assignment."

Jack knew that he should have stopped her once she started about Sam being in love with him but he couldn't make himself do it. Even though he knew he shouldn't and everything told him he couldn't trust anything that the replicator was telling him, he hoped it was telling him the truth. "Why are you telling me this?"

"I thought it could be fun." Replicator Carter moved closer to him. "You know, if you can't have her—"

"Don't even finish that thought. You are not Colonel Carter. And besides, you are a damn evil machine. Never going to happen. Now where is she and what have you done with her?"

"Who says I have done anything with her?"

"You are wearing her clothes."

"I am. Perhaps she gave them to me."

"She didn't. Tell me the truth now or I'll—"

"You'll what?" RC smiled sweetly at him. "I need to go and you are going to let me. Otherwise your dear Samantha Carter will die." She picked a device out of her pocket, pressing a button.

"What is that?"

"I press this one more time—Boom! Now take me through the Stargate."

"No."

"Excuse me?"

"Carter would rather die than let you through that gate."

"But you love her."

Jack ignored the statement. Instead he met RC's eyes steadfastly. "She would rather die."

Staring at him for a moment, RC did a roundhouse kick and then flew out of the room. She made it through the gate.

Jack was plagued by what RC had told him but decided to keep it quiet, for the moment.

Up next, Jack has a surprise for Sam. What is it? Was RC telling him the truth? And if so, what does it mean for Jack and Sam?


	2. Chapter 2

Sorry it has taken me so long to update—my computer was stolen at a conference and I just got it back. I promise to update every other day if not every day until it is finished. Enjoy!

Chapter Two

Two weeks later Sam was off on a weekend vacation spa that she had won. Pete was working and could not join her so she was on her own. She had initially grumbled about being gone for the weekend, as there was a lot of work to be done; however, Sam knew that she could use the rest.

She checked into her room and was astounded at the size and space of the suite. It even had a jacuzzi. She was about to check out the master bedroom when the door opened. Sam immediately reached for her weapon.

"Relax Carter."

She stared. "Sir, what are you doing here?" Then, "I didn't really win this weekend retreat, did I?"

Jack smiled. "No, you didn't. Though everything is paid for so I expect you to enjoy yourself. I can't stay long." Willing himself to stay calm, Jack took a step toward her. "I apologize if I'm wrong and if I am, then we never have to mention this."

"Wrong about what sir?"

"For the next couple of minutes, it's Jack Sam. Jack." Then without any other warning, he closed the distance between the two of them and kissed her.

Shocked Sam opened her mouth. "Samantha," Jack sighed as he deepened the kiss.

"I don't understand," she almost whimpered as he ended the kiss to Jack's pleasure.

"I know that Pete isn't really Pete."

AT that, Sam took a step back. "How? General Hammond doesn't even know…"

"Replicator you. That machine has your memories. She said—if she could be believed—that you were on a special assignment—that George didn't even know. It claimed that you blocked the details more than a couple of other things." Jack searched her eyes carefully. "Was she right? You aren't really with Pete?"

Weighing a couple of different consequences quickly in her mind, Sam kissed him in response. As she rasped out, "She was right. I'm not," Jack pushed her against the door.

"Thank God," he groaned before kissing her again.

When they stopped to breathe, "When did she tell you?" So, Jack gave her the abridged version of what had transpired between them in his office. Still dazed from his kisses, Sam asked in delighted wonder, "You knew that it wasn't me right away?"

"I did," he didn't hesitate.

"But—"

"That machine may look like you Sam but it's not you. I don't know if I could explain it in a way that makes sense but the minute that damn thing entered the room—more like sashayed, I just knew that it wasn't you." He kissed her lightly. "I'll quit as soon as this mission of yours is over."

"Sir- "

"No arguments Sam. The President let a civilian run the SGC before, he'll let me."

"And if he doesn't?"

"It'll be worth it. You are worth giving it all up. Come here," he kissed her again quickly. "I have to go but enjoy the weekend."

Still not quite believing that she wasn't dreaming, Sam stopped him at the door. "Thank you for this."

"You deserve it." Jack smiled as his eyes lingered on the jacuzzi.

Sam followed his gaze and gulped. "I wish you could stay."

"I do too. But we can't. Not yet." They kissed a couple more times before he left, both with smiles on their faces.


	3. Chapter 3

Sorry this is later. I went to post Chapter four and realized that Chapter three didn't get posted. Chapter Five will be up soon. Please review!

Chapter three

Several hours after leaving Sam at the hotel, Jack was on his way through the Stargate to a Tokra site where he had been told Jacob was. He was greeted by some Tokra he did not know and led to a lab to find Selmac discussing some science thing with Annise.

"Jack," Jacob's voice rang after a couple of moments of observed silence. "What brings you to our part of the world?"

"I was hoping to have a word in private with you."

"Oh?"

"It's a-uh personal matter. Everything is ok but it involves your daughter."

Jacob was immediately on the alert. Senses that he would not have had so strong without Selmac sprang through him and he realized that though he did his best to hide it, Jack was a bit nervous. And…maybe even afraid? Though it did not appear to be a kind of scared that threatened the galaxy.

Annise seemed to sense it to as she nodded at Jacob and went back to work. Jacob joined Jack for a walk outside.

"So what's this about Sam?"

"I found out some things recently that I'm technically not supposed to know. George doesn't even have clearance—at least he didn't when he was OIC of Cheyenne. Carter isn't sure if he knows now."

"And how did you find out?"

"We had a bit of a situation a couple weeks ago. A human replicator was formed in your daughter's image. From when she was held by Fifth—seems the damn machine fell in love with your daughter and upon realizing that he couldn't have her, he made her. The replicator had all of her memories at that point in time and in order to try to gain some level of trust with us, let a couple of things slip."

Jacob took a look at him. He knew what he was alluding too, at least he thought he did. "Did that cause any problems?"

"Not in the way you are thinking. However, I realized that I needed to do something if," Jack hesitated.

"I would say that you were afraid you would lose her but you've never really had her. And last time we talked, she seemed to be pretty serious about this guy Pete."

Jack looked around—he knew that he was breaking regulation but Jacob did deserve to know the truth and the way things were going, Jack was not sure the next time they would be able to talk about this. Besides, technically no one knew he knew so… "The thing is Jacob, Pete isn't really Pete. I don't know his real name but they're not really a couple. It's a mission."

Jacob's eyes went wide as he mouthed an "Oh."

They walked in silence for a moment while Jack collected his thoughts. He liked Jacob and he knew Jacob liked him. Still, he felt like a schoolboy meeting his date's father for the first time to take her to the prom. "I asked her to let me know when it was over and I would quit."

Jacob did a sharp look at him.

Jack gave a chuckle. "Yeah, I know. But the President let a civilian be in charge before so I'm hoping…And if not, I'm getting old anyway."

"So you and Sam…"

"I'd like your blessing to marry her."

Jacob shook his head wryly. "You know, I knew there was something there between you the first time we met." He reached around his neck and pulled out a necklace with a ring on it. "It was her mother's."

"Thank you."

"I'd like to be there for the wedding, if possible."

"We'll do our best to coordinate it with you."

They started to make their way back to the gate. "And Jack?" He turned. "I know this goes without saying, but I'm going to say it anyways. You hurt my baby, I will hunt you down. You will die."

"I would expect nothing less."

They shook hands then Jack dialed the gate home. He hoped that the mission was over soon.


	4. Chapter 4

Chapter 4

Sam was preparing dinner. Pete was going to be coming over and they were going to go over the latest on their assignment. Something was off. Sam could feel it. They were so close yet just not close enough. With Daniel on the Prometheus, General O'Neill had given her and Teal'c a couple of days off.

She shook herself. It was hard to think of him of "General" or "Sir" after he had admitted his feelings for her. Only a week had passed since then though to Sam it seemed like an eternity.

She wanted this to be over so badly so that she didn't have to hide how she felt anymore, especially now that she knew he still felt the same way. Sam was beating a little too hard on her food.

"Whoa there. What did that piece of meat do to you?"

Sam turned and sighed. "Sorry. I'm just really frustrated." She looked at it. "I guess that's out." As she tossed the meat in the trash, "Pizza?"

"Sounds like a plan to me. Why don't I order while you clean up?"

They settled down roughly thirty minutes later with beer, pizza and lots of files. "What are we missing?" Sam grumbled.

"I wish I knew," Not Really Pete (NRP) replied. "There's got to be something we are not seeing."

"That's what I keep telling myself. It's almost like there's a part of the puzzle we're not seeing. I would say another player but that player would have to leave some trace. I'm just not seeing it."

"Don't be too hard on yourself Sam. It's one of the reasons we were selected for this assignment. No one else has seen the missing puzzle piece yet either."

"While that is true, I should have been able to get somewhere by now given my history with this group and Michael."

NRP stared at her. "That's the first time I've heard you mention your history."

"I know I should have sooner-"

He waved her off as he took a sip of his beer. "Don't worry about it. I was briefed on what you went through. I also know your jacket and believe I've gotten to know you a bit by now. If it there was a legitimate need for you to mention it, there is no doubt in my mind that you would. On the other side of the coin, I KNOW what they did to you. Not talking about it is completely normal."

Sam offered him a small smile. "Thanks for that." She gave an involuntary shake. "Lately, I haven't been able to get it off of my mind. I have this odd suspicion that Michael is playing an angle, that he knows that we're on to him and somehow he's got this master plan-I know it sounds ridiculous but…"

"It wouldn't be the first time they were ahead of the rest of us."

"No, it wouldn't," she sighed.

"So what are we going to do about it?"

"I wish I knew."


	5. Chapter 5

Just a brief interlude that came to me while I was at work.

Chapter Five

While most of the SGC was asleep that night a phone call was made. "It's me."

"I was expecting a phone call sooner."

"Sorry—it couldn't be helped. And I couldn't get away. The team is feeling the pressure."

"But they aren't on to us?"

"Not in the least. They suspect you have something planned but have no idea how much danger she actually is in."

"Good. We're coming close."

"I know."

"Regrets?"

"I don't have the luxury."

The other voice went deathly dark. "No you don't."


	6. Chapter 6

So, this was what was supposed to be my chapter five, enjoy! And thanks for the reviews!

Chapter Six

Sam walked into the meeting room. "What's the latest sir?"

"Still no word. I knew I shouldn't have let him go."

"Sir," Sam gave him a look.

"What? I'm just sayin'."

"The Prometheus would still be missing if Daniel hadn't gone."

"That is true O'Neill."

Jack glared at Teal'c. The Jaffa met his glare with a raised eyebrow. "Well, it wouldn't necessarily be our problem."

"Please sir," Sam rolled her eyes. "Especially with General Hammond at command you would make it our problem."

Jack stared at her for a moment then relented, "Well, ok, that may be true. But mark my words—Daniel had something to do with this. You know that he can't keep himself out of trouble." No one argued with him. "So-idea? Anyone?"

"We could—no, never mind.

"Colonel Carter?" one of the other officers' present spoke.

"I just figured out why what I was going to suggest wouldn't work based on what we've already tried."

"So, figure a way around the damn problem." Sam stared at Jack. "You know, like you always do."

She stood. "Well, then, I have some work to do. With permission, General."

"Go—dismissed. Everyone. Someone just find that crew!" Jack watched as everyone filed out save one. "Something on your mind Teal'c?"

"Indeed O'Neill."

Jack waited—to be met by silence as Teal'c appeared to be studying him. "Well? Spit it out already. I don't have all day you know."

"Very well then. Colonel Carter."

"What about her?" Again silence. "Teal'c, buddy, I'm really not in the mood for one of those conversations where you speak in metaphors until I catch on to what you are saying. Nor do I have the time. Spit. It. Out. Already."

"As you insist. If I did not know better, I would say that you and colonel Carter have acted on your feelings for each other."

Jack stopped in his tracks and slowly turned to face Teal'c. "What! She's dating Pete. Not to mention regulations for cryin' out loud!"

"I am aware of both of those facts O'Neill. Which is why I said if I did not know better. Colonel Carter would never cheat. And both of you have chosen your careers and the fate of this planet as well as the universe as we know it over your feelings for each other multiple times."

"So why did you bring it up?"

"Because something has changed. And you are like a brother to me O'Neill. I do not know what has changed but something has."

Jack raked a hand through his hair. He had a fleeting thought of telling Teal'c the truth but dismissed it as soon as it was being formed—he couldn't. something had changed though. If Teal'c had noticed it…no, Jack was certain no one else had. Still, he recognized the warning. "I appreciate it Teal'c but nothing has changed between Carter and myself. And now is definitely not the time to be discussing this."

Teal'c bowed his head in acquisition before departing, leaving Jack wishing he could say that things had changed. He wondered if she had made any progress with Pete on whatever their mission was. He thought about asking her, all the while knowing he couldn't. still, the memory of their kisses made him smile. He left the meeting room, heading for his office, feeling a little more upbeat than he thought he would, given the circumstances.

It was a couple hours later when Daniel contacted the SGC, letting everyone know they were OK and heading home. Upon hearing the news, Sam left and headed home for a "date" with Pete. The SGC staff had put in a lot of extra hours (not that anyone minded and in truth, all were comforted in knowing the same would be down for them) for the Prometheus crew and they were due to go home.

Feeling rather good about Daniel and General Hammond, along with the rest of the crew, being ok, coming home safely, Sam found herself humming as she unlocked her door and walked into her house. She was met with a slap on the back of her head.


	7. Chapter 7

Chapter 7

Sam awoke to handcuffs on each of her wrists and ankles. She was also naked. Sam felt some tingling on her stomach but couldn't tell what it was. She tried to focus her eyes. When she heard laughter behind her, her entire body froze.

Jack couldn't explain it. He felt that Sam was in trouble. There was just something in the pit of his stomach that told him she needed him. He called her cell and her house—no answer. He called Pete—no answer. Jack told himself he shouldn't worry. With both Sam and Pete not answering, they could be on their mission.

Still, not sure if Sam had told whoever Pete really was that he knew, he played dumb when leaving a message. "Hey, Pete it's Jack. Listen, I know Sam's probably with you and she does deserve the time off. You know I practically have to force her to take vacation time so I hate to interrupt her but we're having some issues with this new science doo hickey that we picked up from her dad. I could really use her help—all it needs to be is just a quick call in to talk to one of those other Brainiacs in the lab. So, have her call—thanks."

It was only after he hung up that Jack realized that he wasn't at the SGC so if she did call… Growling, he called the skeleton crew and made up a question for them to ask Carter and get back to him. Where was she?

The next day, still no news from Sam. Still worried, Jack called Mark then Daniel—giving them both the same line he had given Pete. Around 1000 that morning, Jack was beginning to get even more worried. He couldn't shake the feeling that Sam was in trouble.

He got dressed and went over to her house. He called Pete again—no answer. He went to Pete's house—no one was there.

Jack went to a pay phone close by and made a call. As he was about to get back in his car, he got a phone call from an unrecognized number. "Hello?"

"Jack, it's Pete. Sam asked me to give you a call. We just got back to my place. Went away for the night. Both of us left our phones at home. She's unloading the groceries now. Did you still need her help with whatever alien technology you guys were playing with?"

"No, we figured it out. Thanks for letting me know. Have her give me a call later though—I'd still like to get her opinion on what we did wrong."

"Of course, I will. Did you want to talk to her now?"

"No, it can wait." Jack heard, "He said he's good" then "Tell him I'll see him at work." "Ok, then. You two enjoy the rest of the day."

"Will do. Bye Jack."

"Bye Pete." Jack hung up, once more sensing that something was not right—for he was staring at Pete's (supposed) place down the street from where he had made the pay phone call. There was no car in the driveway.

NRP looked at Sam in the hospital bed after he hung up the phone. "I'm sorry we had to lie to him."

Sam nodded. "There would be nothing he could do anyway."

"I am so sorry Sam. I should have been there."

"He grabbed me from my home—there's nothing you or anyone else could have done. We didn't even know he was here."

"You know if Michael is here…"

"Then the rest of them are too." Sam closed her eyes in pain.

"What are you going to tell them?"

"Nothing. None of my scars are visible."

"I'll move in or you can move in with me."

"Don't be ridiculous." She sat up. "I'll put a new security system in—tell everyone someone broke into my house while I was gone—which is true. And until this is over, I'll be more diligent when I'm by myself."

NRP shook his head. "I can't believe how calm you are."

"I've been tortured before. The goul'd, Fifth—they're worse than anything Michael can throw at me—or his group. I'm fine. Honest." She reached to squeeze his hand. "I promise."

He grumbled but stood and kissed her head. "I suppose you want to get out of here."

Sam smiled. "You know me so well."

"Let me see what I can do about that."

As soon as he was gone, Sam moved to get to work on the computer in her room, every now and then wincing in pain.

Next, a conversation and some fluff with Sam and Jack. I needed it after this chapter!


	8. Chapter 8

Chapter 8

Jack got his key from the hotel clerk and walked inside. Sam was in a bathrobe sitting on the bed, staring off in to space as he did so. His heart tore as he saw her reach for her weapon as he came in then visibly relax as she realized it was him. Jack locked the deadbolt then was at her side. "What happened?"

"I was captured. The SOB showed up in my home." Jack moved closer to her. "I'm ok—I've been through worse." She looked at him; her eyes threatening tears tore at him. He pulled her towards him. "Can you just hold me tonight?"

"You have to ask?" He moved both of them down on the bed. She leaned into his chest, letter her tears slowly come. Jack just held her silently as he gave her her space. At feeling her shiver, jack sat up and moved the covers down. He took off his shoes, turned off the lights then gathered her in his arms. "I'm not going anywhere." He kissed the top of her head.

Sam smiled slightly. "Thank you…sir." She added the sir almost as an afterthought, trying to keep it as professional as possible between them, given the circumstances.

Jack let her get away with it, given the circumstances. "Try to get some sleep."

She nodded, bringing his arm tighter around her. Sam closed her eyes but Michael was all she could see. A part of her wanted to break the regs and have Jack give her a memory that would make everything bad and evil that she had ever been through disappear. She knew he could. But she also knew that they both would feel a bit…what is the word?...guilty?...about breaking regs. So, Sam decided she would settle with him holding her.

His arms and legs entwined with hers were already radiating positive sensations in place of the negative ones. She let her fingers play with his. She listened for his breathing and he knew he would not let himself fall asleep until he was certain that she was asleep.

Sam kissed his arm. "I wish I could tell you everything."

"You don't need to worry about that. You know I'll always be there for you, no matter what."

Sam smiled. "You've said that to me before."

"I have?"

She nodded. "When I was hallucinating on the Prometheus. I imagined all of you and my dad." Dad was spoken somewhat sadly. "It's been a while since I've seen him."

"Yeah, I miss dad too."

Sam couldn't help but giggle. "I love that you call him that."

"In truth, ever since your dad became a Tokra." Jack couldn't help the slight disdain in his voice, "he's been like family." He wanted to add that he essentially was family now but didn't want to give away that surprise yet.

She turned and looked up at him, surprising him with her next words, "You know, I never told you how sorry I was about your experience in blending."

There was something in the way she said it that caused Jack to narrow his eyes as he propped himself up on his side beside her. "Why would you be sorry?"

"I was the one who asked you to do it."

"Now hold it just a minute there. Saving my life was my decision."

"Was it? I practically begged you to forget your 'Over my dead body' stance. Had anyone else asked you..." her voice trailed off.

It was a question and it wasn't. jack couldn't lie to her. He knew what she was saying was true.. he would rather have died than blended. Until he had seen the look in her eyes as she begged "Please, sir." Still, knowing what could be soon, he gave her what he hoped was his most reassuring smile as he traced her face. "I would do it all again—Ba'al included to be where we are now—with the possibility of the future together."

Sam's heart melted even more for him as she heard the truth in his words, saw it in his eyes, felt it in their closeness. She reached up, kissing him. Jack deepened the kiss as he moved closer to her, his arm brushed her side causing her to gasp in pain.

Both pair of eyes flew open. Jack couldn't help but see some of her scars. He met her eyes. "how did you get free?"

Sam shivered again. "He actually let me go. His taking me was to start to mess with me. Try to get inside my head." Sam raised up a little. "The thing that's really been bugging me-"

"The thing?" Jack looked at her.

"OK, the main thing. Is how did he get in my house? I change my code every couple of weeks. Somehow he knew my code—I checked with the security company. It was my code not the friends and family one that he put in. which means he found a way to see the code. While I was in the hospital, a team found a video bug by my front door. Someone I let in my house is in with him. That has to be the only solution. But who? Who do I trust?"

Jack was silent for a moment. "I have some information too. Though I don't know what it means since I don't know everything." Sam nodded for him to continue. "When I couldn't get a hold of you or Pete I was worried. I tried not to but I felt something was wrong. So, I called a friend. I didn't give details but I wanted him to check. Less than ten minutes after we hung up, I got a phone call from Pete."

"From the hospital," Sam nodded. "We got a phone call saying we had to do something about you trying to get in touch with me."

"He doesn't know?"

"That you know? No one does. I thought it was best to keep it that way."

"Probably is. Though if someone is connected to your target, you need someone to check your house that is not connected to the case."

"I thought of that but what reason could I give?"

"Don't worry. We'll think of something." He brought her closer to him, settling her back down. "We always do—well, at least you do."

Surprising herself Sam replied, "I wish I could just stay with you."

Jack smiled as he kissed her head. "As much as I would love that, what about staying with what's his name—fake Pete?"

"He offered. But I couldn't. I trust him but staying in the same room as him for the rest of this mission. I wouldn't survive. He snores." Jack laughed. "And it's a heavy one—like he's trying to blow out a forest fire."

Jack laughed again. He brought her hand up to his lips. "Still, you should get some sleep. We can talk more in the morning."

Sam looked up at him. "Thank you for coming."

"As if I could stay away. How did you send me that text anyway?"

Sam grinned. Her reply caused Jack to grin too, "I hacked my hospital room's computer."

"That's my girl. Now get some sleep. Don't make me make it an order."

"Yes sir." She giggled as she gave him a mock salute before settling into to his chest and closing her eyes to what was remarkably the best sleep she had had in a rather long time.


End file.
